Honda Repair: 1989 Honda Civic SI, intake manifold gasket, valve cover gasket

Question
Hi.  I am working on an '89 Honda Civic SI that we just purchased.  When we first got it, it was smoking really bad and missing horribily.  I have replaced a messed up head gasket, Intake manifold gasket, valve cover gasket, spark plugs, spark plug wires, and the timing belt.  It is still smoking but not quiet as bad and the car is still missing pretty bad.  The missing gets worse when the car warms up.  I am racking my brain about this and can not figure out what it could be.  Can you help?  Any ideas?
Thank you and I look forward to hearing from you.

Answer
Gregory:
You did not say if you pulled the rings, seals and basically rebuilt the engine when you pulled the head, if not you will end up making the problem worse.
Let me know to what extent the engine was rebuilt and I will try to help from there.
Bill